diff --git a/container/Makefile b/container/Makefile index 13eb6a13..eb63bdb8 100644 --- a/container/Makefile +++ b/container/Makefile @@ -34,7 +34,11 @@ remote_containers := ncbi-amrfinderplus.sif \ snippy.sif \ sourmash.sif \ spades.sif \ - tbprofiler.sif + tbprofiler.sif \ + virulencefinder.sif + +# URLs to Docker containers +DOCKER_bonsai-prp := docker://clinicalgenomicslund/bonsai-prp:0.4.0 # URLs to remote containers URL_ncbi-amrfinderplus := https://depot.galaxyproject.org/singularity/ncbi-amrfinderplus:3.11.11--h6e70893_0 @@ -83,11 +87,9 @@ $(remote_containers): $(call log_message,"Downloading remote container $@ ...") $(eval tool := $(basename $@)) $(eval container_url := ${URL_${tool}}) - version=$$(echo ${container_url} | grep -oP "([0-9]+\.)+[0-9]+") \ - && output_file="${tool}_$${version}.sif" \ - && echo "Downloading $$tool as $$output_file ..." \ - && wget -O $$output_file ${container_url} --no-check-certificate \ - && ln -sf $$output_file $@ + output_file=$$(echo ${container_url} | sed -e 's#https://##' -e 's#/#-#g' -e 's#:#-#g').img \ + && wget -O $${output_file} ${container_url} --no-check-certificate \ + && ln -sf $${output_file} $@ # ---------------------------------------------------------------- @@ -103,7 +105,7 @@ else $(eval tool := $(basename $@)) $(eval container_url := ${DOCKER_${tool}}) @chmod o+w $(INSTALL_LOG) \ - && output_file=$$(echo ${container_url} | sed -e 's#https://##' -e 's#/#-#g' -e 's#:#-#g').img \ + && output_file=$$(echo ${container_url} | sed -e 's#docker://##' -e 's#/#-#g' -e 's#:#-#g').img \ && sudo singularity build --force $${output_file} ${container_url} \ && ln -sf $${output_file} $@ endif